NAME
DistanceEst - Estimate distances between contigs using paired-end alignments.
SYNOPSIS
DistanceEst -k<kmer> -s<seed-length> -n<npairs> [OPTION]... HIST [PAIR]
DESCRIPTION
Estimate distances between contigs using paired-end alignments.
-
Arguments:
- HIST
-
distribution of fragments size
- PAIR
-
alignments between contigs
-
Options:
- --mind=N
-
minimum distance between contigs [-(k-1)]
- --maxd=N
-
maximum distance between contigs
- --fr
-
force the orientation to forward-reverse
- --rf
-
force the orientation to reverse-forward
- -k, --kmer=N
-
set --mind to -(k-1) bp
- -l, --min-align=N
-
the minimal alignment size [1]
- -n, --npairs=NPAIRS
-
minimum number of pairs
- -s, --seed-length=L
-
minimum length of the seed contigs
- -q, --min-mapq=N
-
ignore alignments with mapping quality less than this threshold [10]
- -o, --out=FILE
-
write result to FILE
- --mle
-
use the MLE [default] (maximum likelihood estimator)
- --median
-
use the difference of the population median and the sample median
- --mean
-
use the difference of the population mean and the sample mean
- --dist
-
output the graph in dist format [default]
- --dot
-
output the graph in GraphViz format
- --gv
-
output the graph in GraphViz format
- --gfa
-
output the graph in GFA2 format
- --gfa2
-
output the graph in GFA2 format
- -j, --threads=N
-
use N parallel threads [1]
- -v, --verbose
-
display verbose output
- --help
-
display this help and exit
- --version
-
output version information and exit
- --db=FILE
-
specify path of database repository in FILE
- --library=NAME
-
specify library NAME for sqlite
- --strain=NAME
-
specify strain NAME for sqlite
- --species=NAME
-
specify species NAME for sqlite
AUTHOR
Written by Jared Simpson and Shaun Jackman.
REPORTING BUGS
Report bugs to <[email protected]>.
COPYRIGHT
Copyright 2014 Canada's Michael Smith Genome Sciences Centre